The Souls Saga: Unknowing
by Amz.Idris
Summary: This is the first story of the saga. There will be more from a few other different fandoms that I will mix together. I will post them independently and in one story for those of you who don't mind multiple chapters being on one page. This is SGA's story for ShepWeir. Enjoy! T for mild violence. Comment if it should be changed.
1. Chapter 1

CHAPTER 1

Dr Elizabeth Weir tread carefully across the rough, unfamiliar ground beneath her feet. It was not her first time off world and she had been asked by the leader of a small settlement they were recently allied with to attend the 'choosing ceremony' his daughter was to go through. She had momentarily thought of refusing but quickly dismissed the thought and accepted his offer. Now she was heading toward a village in the middle of a forest with Colonel Shepard's team.

As the village neared, the sight took her breath away. Small wooden huts that seemed to be constructed from long, thin twigs and bound by vines of brightly coloured flowers. It was so beautifully blended with the forest that surrounded them. The villagers similarly wore vines of flowers wrapped around wrists and ankles, small wreath-like head dresses made of the vines sat atop their heads. In the centre of the crowd of people stood the leader's daughter almost encompassed in white vines and flowers. One villager offered each of the 'outsiders' a head dress and a tangle of vines to place on their wrists. Most of them graciously placed the ceremonial dress on however Ronon stared at them with distaste.

"Just put them on, we don't want anyone getting upset." John said in his usual wary tone. Obediently, Ronon put on the vines with disgust. "Thank you. Now that wasn't so hard was it?"

Ronon rolled his eyes and grunted at John before they moved closer to the gathered crowd.

Tyran, the leader of the village, rose onto the stone platform in the centre of the ring of huts, waving his arms and hushing the assembled people. "Mayana, please step forward." The smiling man gestured. The girl in white moved forward and joint her father on the platform, embracing him. In that moment, a small octagonal column rose from the stone, letting off a faint blue light from the panel on the slanted top. "Now, place both hands on the device. Let the ancestors guide you through the next step in life's journey.

"What's going to happen?" John asked curiously in a hushed voice.

"The light will encompass her and the man she is destined to be with." A small elderly woman supplied him. "We all go through this ceremony. It is like a marriage, the two people are joined together in body, mind and soul. The white represents the purity of which each of us must be before we can hope to reach enlightenment. The vines of our growth in this existence."

"Oh, thank you."

Suddenly, Mayana was engulfed in a blue light, as was one of the men in the assembled crowd. A pathway was cleared by the villagers to allow the two to stand together on the platform. As he slowly walked toward her, it was evident that they had love filled hearts and teary eyes.

The old woman continued speaking to them. "This device brings together two people who's hearts have been wholly given to each other. And sometimes it takes until the ceremony to realise it. When the device detects when one of the women is ready for the ceremony, our leader is notified through the window of the ancestors. It is made of glass and yet doesn't break, hanging from the ceiling of the great temple."

Slowly, the light that encompassed them faded and the ceremony continued. "The ancestors have seen into your hearts and selected you for each other. You may now seal your union." The two people shared a deep kiss.

"The kiss represents bond between them." The old woman informed them over the cheering of the crowd. "This is what seals the connection."

Mayana, her father and her new husband all turned to face the gathered throng. Cheers filled the air as they walked amongst family and friends who congratulated the two.

Tyran moved swiftly through the crowd to greet the atlantis team. "Thank you for joining in this celebration. My daughter would not stop begging for me to send you the invitation."

"It was an honour to he here, Tyran." Dr Weir thanked.

"Will you join us in our celebratory feast?" He asked, gesturing to the large hall that many people gravitated toward. "I am sure that my daughter would understand if you had to leave so soon after the ceremony."

"Of course we will join the celebration." She stated as if it were obvious to everyone.

"You are no longer required to wear the ceremonial dress." He said, talking the wreaths of flowers from his body.

Ronon instantly ripped the flowers off him and went to hug Tyran. "Thank you."

"You are most welcome." Tyran said, patting Ronon on the shoulder. "Please, come." He spoke to the assembled group and led them to the hall.

"We were wondering if we could study your device. Something like that must be incredibly complex. We're trying to understand everything about the Ancients so that we can better understand the technology we found in the city of the ancestors." Dr Weir asked before she and Tyran entered the hall.

"I will have to consult several of the villagers before I can give you an answer but for everything that you have done for us, I do not see why they will refuse." 


	2. Chapter 2

CHAPTER 2

After many hours of celebration, Dr Weir took the surprisingly sober team back to Atlantis. Dr Mckay had been bombarding her with every theory he had and requests for all of the equipment he would need. In the end she had told him to gather anything he thought appropriate and to write a preliminary report for her before he left.

"Colonel Shepard, can I speak to you for a moment?" She asked.

"'Course." He followed her into her office.

"What do you think about the device?" She asked him, looking directly into his eyes.

"Personally, unless we can use it to kill some wraith then I don't see the point of wasting 48 hours on it." He said bluntly. "I know that we should be finding out everything about the ancients but there is no way that I can see that device actually helping us."

"I know, but Rodney seems to think that they can use it is some sort of a lie detector if it works one of a million ways he thinks. Anyway, if that helps us understand the circuitry of a weapon here on Atlantis then it would have been worth it." Dr Weir explained.

"It's just going to cause us more trouble than it's worth."

"I hope that you're wrong. Why don't you get some sleep, you ship out in 10 hours."

"Goodnight Elizabeth." He spoke in the way he saved just for her, full of everything that shouldn't be there. But is.

As he walked away, Elizabeth leaned back into her chair and took a deep breath. She hated the thought of seeing him go through the gate again, it hurt that little bit more every time she had to do it. Clearing her head of the melancholia that subject always brought, she took her laptop from where it sat on her desk and slowly made her way down to her room. 


	3. Chapter 3

CHAPTER 3

"So far Mckay thinks that he's onto something but I'm not so sure. He's been looking at the thing for twelve hours and hasn't made any significant progress." The voice of John Shepard crackled over the radio. "Also, Tyran wanted to speak with you. I don't know what about but he said that it was a matter of 'great urgency'."

"I'll be there as soon as I can. Anything else to report?" She asked.

"It's quiet on our end."

"I'll be there in 10 minutes. Weir out."

"Copy, Shepard out." With that the transmission went dead and the stargate disconnected.

After gearing up in a basic vest, radio and side arm, Dr Weir stepped through the gate to see Colonel Shepard on the other side. "Are you sure that he didn't say anything else?" She asked, itching to know what was going on.

"Not a word." Colonel Shepard explained indifferently.

After trudging through the now familiar surroundings, Dr Weir, accompanied by John and Teyla, entered Tyran's, now empty, hut. "You wanted to see me?"

"Yes, you must come to the temple quickly." Tyran beckoned, leading them through the dense vegetation that surrounded the temple. They burst through the opening in the doorway and marvelled at how alike the 'temple' was to Atlantis. A large screen lit up once they had stepped inside, which showed Dr Weir's face and a long list of ancient symbols next to it.

"We have always been able to read the language of the ancestors." Tyran explained plainly. "This shows that you are ready. However, many villagers say that you should not be allowed to go through the ceremony. They believe that it was a gift to our people and while we have allowed you to study it, the ceremony is a deep root of our society, no outsider has ever taken part in the ceremony and should thus stay that way." Tyran's face dropped into a mournful smile.

"I don't see why I was called here then." Dr Weir thought aloud, hoping to push further explanation from the man.

"If they see that you are in the window of the ancestors then they may allow you to go through the ceremony however, before that would be able to happen, you need to acknowledge this and search within yourself to discover if you are truly ready." Tyran explained with a cautious smile on his face. "Also, if this man is of your home world then there is no way that you can go through with the ceremony. They have to be present in the village at the time."

"I'm not sure if I want to be part of this ceremony. Some things are best left alone and I think that this is one of them, if the person is on Atlantis then one or both of us may risk losing our place on the expedition." Dr Weir explained, trying as hard as she could to keep her eyes solidly on Tyran.

"Please, think of what this could do. You have no way of knowing yet of the impact until you have gone through the ceremony." It appeared as if Tyran desperately wanted her to carry through with it. "Nobody has ever rejected their opportunity to take part in the ceremony and our people have been carrying this out for thousands of years."

"I will consider taking part in the ceremony but I will need time, and possibly lots of it." Dr Weir resigned. She wasn't sure if she wanted to risk the chance that Colonel Shepard was actually the person her heart was supposed to have 'chosen'.

"Thank you Dr Weir, but I believe that you will chose to take part in the ceremony." 


	4. Chapter 4

CHAPTER 4

"Elizabeth, do you want to do this?" John asked her for the 52nd time in the last hour (It wasn't as if she was counting).

"No." She finally gave in, she did not want him to know how she felt. But the machine would know if he loved her back right? It wouldn't make her go through the ceremony if it wasn't true. Once again she looked at the forest surrounding her. It wasn't comforting to have to make the decision and then take part in the ceremony (if she chose to) immediately after.

"Elizabeth, do you even know who the machine might be talking about?" He asked hoping that she would say him but, unfortunately, she didn't pick up the hidden message in his tone like she always did.

"I think I'll do it anyway, what could possibly go wrong?" She said, knowing that it could mean one or both of them could be transferred off Atlantis. She gave him a weak smile.

"There's something I need to tell you." He said, hoping that she would let him talk. She nodded her head but before he could say anything, their radios buzzed into life.

"John, Dr Weir. Ten Geni soldiers just walked through the gate. They've taken over the village, I am the only one who got away." Teyla's voice spoke over the radio. "They believe the device is a weapon against the wraith. They have their scientists trying to remove it. We need to move swiftly, they are threatening the villagers with the lives of Tyran, Mayana, Dr McKay and Ronon. If we do not act quickly, I believe that they will kill them."

"Thanks Teyla, get to the clearing as quickly as you can. Elizabeth and myself are there already." He sighed internally, he had wanted to tell her how he felt. It was just going to have to wait. 


	5. Chapter 5

CHAPTER 5

It hadn't gone well. Dr Weir was stood with commander Kolya, knife to her throat. John Shepard was once again pointing a gun at them.

"We've been here before Colonel and you both know what I'm capable of. And you don't even have a clear shot this time." Kolya mocked. "She will die if you do not tell me why the device doesn't work."

"It doesn't work because it doesn't do what you think it does." John said in a slightly patronising voice. "It taps into the subconscious of the person using the device and shows them who they're supposed to marry. And even then, they have to be identified by the machine first."

"I don't believe you." He said coldly, digging the point of the knife into Elizabeth's throat. A small trickle of blood slid down her neck. "What did you do to the..."

His words cut off abruptly as a bullet hit him in the back of the head. Teyla, as planned had gone around the edge of the village, but she wasn't fast enough. There was a cut, only a few milimetres wide but very deep, in Elizabeth's neck.

As she dropped to her knees, the colonel rushed over and supported her. She looked like she was in shock but she had no idea why. She wasn't the one who had to point the gun or take the shot. She just stood there, staring at John. Which she was still doing, she was looking up at him past her drooped eyelids.

"You're going to be fine. We'll get Dr Beckett to stitch you back together and you'll be good as new." He said to her while she breathed heavily. "I wouldn't have been able to do it you know."

"Do what?" She asked him, unsure of why he would suggest such a thing.

"Shoot him. You were way too close and the thought of losing you... Well, I don't even want to think what life would be like without you." He started, completely sure that it was time to tell her the truth.

"I love you." She whispered to him. She straightened up to look directly into his eyes. "Probably more than is healthy."

"I believe that was my line." He joked before capturing her lips in a kiss. Oblivious to everything that was around them, they stayed in their little piece of paradise, light encompassing them. 


	6. Chapter 6

CHAPTER 6

They thought that they'd been able to get away with their feelings until they were called back to Earth, a certain General wanted to talk to them. Now, they were stood in the Oval office along with Colonel Carter, Colonel Cauldwell and several other Colonels and Generals that were in command of projects that branched off from the SGC.

"Sit down people, we're going to be here for a while." President Henry Hayes said as he walked into the room closely followed by none other than General Jack O'Neill. "As you know, everyone in this room is a representative of one Air Force organisation or another that requires top level security clearance due to the fact that they all are branched from the Stargate Programme." He started. "Colonel Carter is stepping in for General Landry as he has been called off world. But the rest of you are the superior officers of these projects and commands. We're here today to discuss a change in regulation that has been thought about for the past six years. General, I'll let you take over."

"As some of you will know, there has been tension between multiple people due to ranks." Jack started, glancing at not only the two Atlantis team members but at Sam as well. "There has been one regulation in particular that has caused this tension. The fraternisation regulations." He smiled slightly when he caught Sam's eye. "The president and joint chiefs have agreed that for the people under your command, the fraternisation regulations will be disbanded." It was obvious that he was trying to refrain himself from pulling Sam into a deep kiss but he managed to and continued. "As a result of this change, a superior officer is to clear all relationships and inform myself for review."

"General, would you, Colonel Carter, Colonel Sheppard and Dr Weir please stay behind. The rest of you have some changes to make, dismissed." The President smiled. As the last of the men closed the door, the President's smile became a smirk. "I have you four to thank for all the trouble that this has caused me."

Sam looked as if she was going to start apologising so he cut her off there and then. "I didn't say that I was mad, now. I believe that you have some thing to officially file to me. As you, General and Dr Weir, are commanding officers, you are to report any matter concerning a personal life to me."

"I think I do Mr President." Jack smiled.

"We both do." Dr Weir smiled after John raised an eyebrow at her. 'Let's get this over with.' His voice had echoed in her head. 


	7. Chapter 7

CHAPTER 7

The announcement had gone out that morning and there had been a continual flow of sly questioning to both John and Elizabeth about their relationship. 'Three hours.' She thought, dreading the next hour. 'It's been three hours.'

"Morning Elizabeth." John smiled. She had to put up with the constant questioning from not only the people talking to her, but from John's mind as well. "Shall we go to that lovely briefing you have panned for my team?" He asked with a smile, offering her his hand.

"So we're not keeping our relationship a secret any more?" She smiled, already knowing the answer.

"Nope." She accepted his hand and let him lead the way from her office.

As they walked through the control room, they gained many stares, glances and glances again. It was pathetic really. Chuck did however hand Abigail a large wad of cash before rolling his eyes.

Rodney rolled his eyes when he saw them. "Obviously that's why you were late." He shook his head and flicked the file in front of him open.

"We were late because we've been attacked with questions about our relationship all day. I just dragged her out of her office." John corrected.

"She has a name and a briefing to start." Elizabeth reprimanded before taking a seat. "Hopefully this will be the last time in a few months that you have to go back to M4Y D3X." 


	8. Chapter 8

CHAPTER 8

Rodney was hunched on the floor, trying to repair the damage the Genii had caused while Teyla and Ronon helped rebuild the huts that had been caught in the fire fight. John and Elizabeth were in the temple discussing the not so small matter of the ceremony.

"We've already been affected by the machine and it won't work a second time. You said so yourself." John stated. "Our souls are already one, our minds have been joined and all of that stuff."

"I see." Tyran contemplated. "This is most peculiar. You didn't touch the device?" When they shook their heads his frown grew bigger. "Perhaps it was your proximity to the device. It may have sensed that the two of you were close and activated. Could this be a result of the genii trying to remove the device."

"I guess so, but we've got McKay fixing it right now." John smiled. "He'll have it fixed in no time."

"I hope that you are right." He shook off his pondering gaze and resumed his usual ecstatic nature. "I am happy for the two of you. Please take this." He offered them both a pendant. "As part of the ceremony, it is traditional to offer the other one of these. They will be able to heal the other, they do not require this 'gene' you spoke of."

John put his round Elizabeth's neck, once it made contact with her skin it glowed the same blue as the device and then faded. The same happened when Elizabeth put hers around John's neck. They had no idea what it meant and probably didn't care.

"I hope that you will never have to use them." Tyran smiled to them and gestured for them to follow him out of the temple and back to the village.

Just before they stepped through the event horizon, Elizabeth turned to him; a smile on her face. "I'll never have to worry about you coming back covered in bullet holes."

"So we get all of the dangerous missions now?" He asked hopefully.

"No." She kissed him lightly before taking a final step backwards into the wall of blue.

"Shame." He smiled before stepping through after her.


End file.
